Li Caijuan, Ling Qufei, Ge Chen, Ye Zhuqing, Han Xiaofei
School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, PR China.
School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, PR China.
Gene. 2015 Feb 25;557(2):201-8. doi: 10.1016/j.gene.2014.12.034. Epub 2014 Dec 18.
The large-scale loach (Paramisgurnus dabryanus, Cypriniformes) is a bottom-dwelling freshwater species of fish found mainly in eastern Asia. The natural germplasm resources of this important aquaculture species has been recently threatened due to overfishing and artificial propagation. The objective of this study is to obtain the first functional genomic resource and candidate molecular markers for future conservation and breeding research. Illumina paired-end sequencing generated over one hundred million reads that resulted in 71,887 assembled transcripts, with an average length of 1465bp. 42,093 (58.56%) protein-coding sequences were predicted; and 43,837 transcripts had significant matches to NCBI nonredundant protein (Nr) database. 29,389 and 14,419 transcripts were assigned into gene ontology (GO) categories and Eukaryotic Orthologous Groups (KOG), respectively. 22,102 (31.14%) transcripts were mapped to 302 KEGG pathways. In addition, 15,106 candidate SSR markers were identified, with 11,037 pairs of PCR primers designed. 400 primers pairs of SSR selected randomly were validated, of which 364 (91%) pairs of primers were able to produce PCR products. Further test with 41 loci and 20 large-scale loach specimens collected from the four largest lakes in China showed that 36 (87.8%) loci were polymorphic. The transcriptomic profile and SSR repertoire obtained in this study will facilitate population genetic studies and selective breeding of large-scale loach in the future.
大鳞副泥鳅（Paramisgurnus dabryanus，鲤形目）是一种底栖淡水鱼类，主要分布于东亚地区。由于过度捕捞和人工繁殖，这种重要水产养殖物种的天然种质资源最近受到了威胁。本研究的目的是获得首个功能基因组资源和候选分子标记，用于未来的保护和育种研究。Illumina双末端测序产生了超过一亿条 reads，组装得到71,887条转录本，平均长度为1465bp。预测出42,093条（58.56%）蛋白质编码序列；43,837条转录本与NCBI非冗余蛋白质（Nr）数据库有显著匹配。29,389条和14,419条转录本分别被归入基因本体（GO）类别和真核直系同源组（KOG）。22,102条（31.14%）转录本被映射到302条KEGG通路。此外，鉴定出15,106个候选SSR标记，并设计了11,037对PCR引物。随机选择400对SSR引物进行验证，其中364对（91%）引物能够产生PCR产物。对从中国四大湖泊收集的41个位点和20个大鳞副泥鳅样本进行进一步检测，结果表明36个（87.8%）位点具有多态性。本研究获得的转录组图谱和SSR库将有助于未来大鳞副泥鳅的群体遗传学研究和选择性育种。
